AutoCloner

Multiple sequence alignment - TraesCS5B01G235000

Loading Multiple Alignment...

Download Multiple Sequence Alignment: (Fasta) (Clustal)

BLAST Results

Shown here are the results of a BLAST search against the genome using the input sequence. The pipeline uses this to extract flanking regions for cloning. If the result of the multiple sequence alignment is not as expected, these results could be used for further investigation.

	qseqid	sseqid	percentage.identical	alignment.length	no.mismatch	no.gap.openings	qstart	qend	sstart	send	evalue	bitscore
0	TraesCS5B01G235000	chr5B	100.000	2548	0	0	975	3522	414827854	414830401	0.000000e+00	4706.0
1	TraesCS5B01G235000	chr5B	100.000	680	0	0	1	680	414826880	414827559	0.000000e+00	1256.0
2	TraesCS5B01G235000	chr5D	95.784	2467	80	11	1017	3477	351785775	351788223	0.000000e+00	3958.0
3	TraesCS5B01G235000	chr5D	82.908	509	48	18	1	474	351774571	351775075	4.200000e-114	422.0
4	TraesCS5B01G235000	chr5D	86.893	206	13	7	475	680	351775116	351775307	5.920000e-53	219.0
5	TraesCS5B01G235000	chr5A	95.943	2317	63	11	975	3289	452109216	452111503	0.000000e+00	3729.0
6	TraesCS5B01G235000	chr5A	86.580	693	54	22	3	680	452108506	452109174	0.000000e+00	728.0
7	TraesCS5B01G235000	chr5A	94.545	220	11	1	3302	3520	452111762	452111981	4.350000e-89	339.0
8	TraesCS5B01G235000	chr5A	75.769	260	39	16	3211	3458	445133902	445134149	3.720000e-20	110.0
9	TraesCS5B01G235000	chr6D	76.707	249	32	19	3227	3467	270587082	270586852	7.990000e-22	115.0
10	TraesCS5B01G235000	chr6B	88.372	86	10	0	3373	3458	423193472	423193557	1.730000e-18	104.0
11	TraesCS5B01G235000	chr4A	81.395	129	21	3	3342	3469	533449126	533449000	6.220000e-18	102.0
12	TraesCS5B01G235000	chr4A	83.333	108	15	3	3373	3478	539132342	539132236	2.890000e-16	97.1
13	TraesCS5B01G235000	chr4B	80.147	136	20	7	3335	3469	93286317	93286446	1.040000e-15	95.3
14	TraesCS5B01G235000	chr7A	83.019	106	14	4	3373	3475	700824069	700824173	3.740000e-15	93.5
15	TraesCS5B01G235000	chr1D	91.304	46	4	0	1099	1144	426595153	426595198	2.940000e-06	63.9
16	TraesCS5B01G235000	chr1A	91.304	46	4	0	1099	1144	521639874	521639919	2.940000e-06	63.9
17	TraesCS5B01G235000	chr1A	77.500	120	18	8	3302	3414	526921442	526921325	2.940000e-06	63.9
18	TraesCS5B01G235000	chr3A	100.000	30	0	0	1115	1144	498229371	498229400	4.910000e-04	56.5

These results show the homologous regions that are presented in the multiple sequence alignment. HSPs from the BLAST search that are within 2000 bases of each other have been grouped together. Homologous regions that are purely upstream or downstream may be removed if they don't overlap both primers.

	query	scaffold	start	end	length	rev.comp	avg.bitscore	max.bitscore	avg.percent.identical	query.start	query.end	num_hsp	groupid	homo_length
0	TraesCS5B01G235000	chr5B	414826880	414830401	3521	False	2981.000000	4706	100.0000	1	3522	2	chr5B.!!$F1	3521
1	TraesCS5B01G235000	chr5D	351785775	351788223	2448	False	3958.000000	3958	95.7840	1017	3477	1	chr5D.!!$F1	2460
2	TraesCS5B01G235000	chr5D	351774571	351775307	736	False	320.500000	422	84.9005	1	680	2	chr5D.!!$F2	679
3	TraesCS5B01G235000	chr5A	452108506	452111981	3475	False	1598.666667	3729	92.3560	3	3520	3	chr5A.!!$F2	3517

AutoCloner calculated primer pairs

These primer pairs were selected by Autocloner to minimize primer penalty (calculated by Primer3), whilst remaining within the specified product range where possible.

Download AutoCloner chosen primers as CSV: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Hairpin	End Stability	Orientation
32	33	1.444553	CTGTCGTGCGGTCTCCTTC	60.445	63.158	0.00	0.00	3.46	F
581	684	1.589196	CTCCCGAATCCGAGCGAAC	60.589	63.158	0.00	38.22	3.95	F
2119	2222	2.690653	CTTCAACGGCCACCCCAAGA	62.691	60.000	2.24	0.00	3.02	F

Position	MSA Position	Penalty	Sequence	TM	GC	Hairpin	End Stability	Orientation
1858	1961	3.250762	ACGACATGATTTATTGCATCCGG	59.749	43.478	0.00	5.14	R
2145	2248	3.102515	GCACAGAGCAGCAAACATG	57.897	52.632	44.79	3.21	R
3462	3817	3.504343	GCCTGGGTAGAATATACTCCCCT	60.504	52.174	37.03	4.79	R

All possible primers

Listed here are all possible primers based on the multiple sequence alignment and SNPs generated previously. A lower penalty score indicates a better primer. If the AutoCloner primers did not work during PCR or sequencing, these could be used as alternatives.

Download all possible primers: (Forward) (Reverse)

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
32	33	1.444553	CTGTCGTGCGGTCTCCTTC	60.445	63.158	0.00	0.00	0.00	3.46
57	58	6.625081	CGTCACTTTCCCTTTTTGTCTTTCTT	60.625	38.462	0.00	0.00	0.00	2.52
82	83	2.224621	TGGTTGCCCTCTCTCTTCTTTG	60.225	50.000	0.00	0.00	0.00	2.77
116	120	2.125952	CGCGTCACAGATCTGCCA	60.126	61.111	22.83	6.36	0.00	4.92
158	163	5.355910	TCGGGACTATTTGTTAGGCATTTTC	59.644	40.000	0.00	0.00	37.73	2.29
180	185	4.681978	AGTCCAAGACACGCCGGC	62.682	66.667	19.07	19.07	34.60	6.13
181	186	4.980805	GTCCAAGACACGCCGGCA	62.981	66.667	28.98	0.00	32.09	5.69
189	194	2.123988	GACACGCCGGCATTGAACAA	62.124	55.000	28.98	0.00	0.00	2.83
198	203	2.164219	CGGCATTGAACAACTGGCTATT	59.836	45.455	15.15	0.00	33.64	1.73
247	252	2.573462	CAACCCCTTCTTCATCCTCTCA	59.427	50.000	0.00	0.00	0.00	3.27
276	281	5.360999	CCAAGAATTCCTTTTGAGGGGATAC	59.639	44.000	0.65	0.00	31.42	2.24
278	283	6.408770	AGAATTCCTTTTGAGGGGATACTT	57.591	37.500	0.65	0.00	0.00	2.24
353	404	2.489329	CCACGTTTGAGAAGGCATTCAT	59.511	45.455	14.34	0.00	37.94	2.57
360	411	4.403585	TGAGAAGGCATTCATCAGAGAG	57.596	45.455	14.34	0.00	37.94	3.20
362	413	4.468868	TGAGAAGGCATTCATCAGAGAGAA	59.531	41.667	14.34	0.00	37.94	2.87
385	436	5.416271	AAAGAGAAGGCATTCGGTAGTTA	57.584	39.130	5.31	0.00	40.58	2.24
425	479	3.270877	AGGCATTCGGTAGCTAGTTTTG	58.729	45.455	0.00	0.00	0.00	2.44
426	480	3.007635	GGCATTCGGTAGCTAGTTTTGT	58.992	45.455	0.00	0.00	0.00	2.83
527	629	1.745489	CGCTACCCCTGAAACAGCC	60.745	63.158	0.00	0.00	0.00	4.85
578	681	2.573609	AAACCTCCCGAATCCGAGCG	62.574	60.000	0.00	0.00	38.22	5.03
579	682	3.217017	CCTCCCGAATCCGAGCGA	61.217	66.667	0.00	0.00	38.22	4.93
580	683	2.782222	CCTCCCGAATCCGAGCGAA	61.782	63.158	0.00	0.00	38.22	4.70
581	684	1.589196	CTCCCGAATCCGAGCGAAC	60.589	63.158	0.00	0.00	38.22	3.95
582	685	2.954868	CCCGAATCCGAGCGAACG	60.955	66.667	0.00	0.00	38.22	3.95
583	686	3.617538	CCGAATCCGAGCGAACGC	61.618	66.667	11.31	11.31	42.33	4.84
584	687	3.617538	CGAATCCGAGCGAACGCC	61.618	66.667	15.44	6.59	43.17	5.68
585	688	3.617538	GAATCCGAGCGAACGCCG	61.618	66.667	15.44	16.75	43.17	6.46
605	708	4.586334	CCGCACCAAACTTGAAAATTTTG	58.414	39.130	8.47	0.00	43.53	2.44
648	751	2.759795	GCAGCCTCCCACTTTCCT	59.240	61.111	0.00	0.00	0.00	3.36
1858	1961	6.917477	TCATAACTTTGCAAGATTGTGTTGTC	59.083	34.615	16.02	0.00	0.00	3.18
1873	1976	4.142491	TGTGTTGTCCGGATGCAATAAATC	60.142	41.667	7.81	0.00	0.00	2.17
1874	1977	4.013050	TGTTGTCCGGATGCAATAAATCA	58.987	39.130	7.81	0.00	0.00	2.57
2119	2222	2.690653	CTTCAACGGCCACCCCAAGA	62.691	60.000	2.24	0.00	0.00	3.02
2145	2248	2.134789	AGTTTGAGATCCATGGTGCC	57.865	50.000	12.58	2.12	0.00	5.01
2282	2385	7.669304	TGGTTAATTCCTGTGATTTCTCAATGA	59.331	33.333	0.00	0.00	31.85	2.57
2296	2399	6.579666	TTCTCAATGAAGTTGGATTCAAGG	57.420	37.500	0.00	0.00	42.21	3.61
2332	2435	3.669023	GCTTGGAAGAGCTTTTGATCACG	60.669	47.826	0.00	0.00	39.57	4.35
2661	2764	6.791303	TGAATAACTTTGGAGTTGTGTTGTC	58.209	36.000	2.25	0.00	45.46	3.18
2883	2986	4.157246	TGGTTGATAGTGTGGTGACTACT	58.843	43.478	0.00	0.00	31.19	2.57
2913	3017	9.793252	CCTGATAAGACTATTTTGATTTGGTTG	57.207	33.333	0.00	0.00	0.00	3.77
2932	3036	3.895232	TGATGTACTTGGAAGCTCCTC	57.105	47.619	0.00	0.00	37.46	3.71
2992	3096	8.722480	TGGAAACTCTTATACATGAACATCAG	57.278	34.615	0.00	0.00	0.00	2.90
3153	3259	0.242825	TAGTTTCTCCGTGGTCTGCG	59.757	55.000	0.00	0.00	0.00	5.18
3234	3342	6.796705	ACTCCCTTTGTTACGAAATACTTG	57.203	37.500	0.00	0.00	0.00	3.16
3433	3788	5.140454	ACTTAAAGTTGCTTGACTTGGGAT	58.860	37.500	2.30	0.00	39.68	3.85
3462	3817	9.793259	ACCTAGAACTTCAAATATTTTGAGACA	57.207	29.630	12.32	0.00	0.00	3.41
3511	3866	7.630082	TCACTCCAATTAAGTAACAATAGCCT	58.370	34.615	0.00	0.00	0.00	4.58
3516	3871	7.122055	TCCAATTAAGTAACAATAGCCTTGTGG	59.878	37.037	3.25	0.00	32.22	4.17
3520	3875	4.079253	AGTAACAATAGCCTTGTGGTTGG	58.921	43.478	3.25	0.00	35.27	3.77
3521	3876	2.675658	ACAATAGCCTTGTGGTTGGT	57.324	45.000	1.70	0.00	35.27	3.67

Position	MSA Position	Penalty	Sequence	TM	GC	Self any TH	Self end TH	Hairpin	End Stability
14	15	1.444553	GAAGGAGACCGCACGACAG	60.445	63.158	0.00	0.00	0.00	3.51
24	25	1.619332	AGGGAAAGTGACGAAGGAGAC	59.381	52.381	0.00	0.00	0.00	3.36
32	33	4.632538	AAGACAAAAAGGGAAAGTGACG	57.367	40.909	0.00	0.00	0.00	4.35
82	83	4.717313	GTGGAAGTGGGGGACGGC	62.717	72.222	0.00	0.00	0.00	5.68
128	132	5.484715	CCTAACAAATAGTCCCGACTTGAA	58.515	41.667	2.08	0.00	42.54	2.69
158	163	0.868406	GGCGTGTCTTGGACTCAAAG	59.132	55.000	0.00	0.00	33.15	2.77
180	185	5.220662	CGACCTAATAGCCAGTTGTTCAATG	60.221	44.000	0.00	0.00	0.00	2.82
181	186	4.876107	CGACCTAATAGCCAGTTGTTCAAT	59.124	41.667	0.00	0.00	0.00	2.57
198	203	0.813184	CTAACCTCAACGGCGACCTA	59.187	55.000	16.62	0.00	35.61	3.08
247	252	4.085009	CTCAAAAGGAATTCTTGGGAGCT	58.915	43.478	5.23	0.00	35.55	4.09
293	298	3.250762	CGTGGAATGCTCTGTCTCAAAAA	59.749	43.478	0.00	0.00	0.00	1.94
294	299	2.807967	CGTGGAATGCTCTGTCTCAAAA	59.192	45.455	0.00	0.00	0.00	2.44
295	300	2.224281	ACGTGGAATGCTCTGTCTCAAA	60.224	45.455	0.00	0.00	0.00	2.69
296	301	1.344438	ACGTGGAATGCTCTGTCTCAA	59.656	47.619	0.00	0.00	0.00	3.02
297	302	0.969149	ACGTGGAATGCTCTGTCTCA	59.031	50.000	0.00	0.00	0.00	3.27
302	307	3.904136	AAGAAAACGTGGAATGCTCTG	57.096	42.857	0.00	0.00	0.00	3.35
353	404	4.963318	TGCCTTCTCTTTTTCTCTCTGA	57.037	40.909	0.00	0.00	0.00	3.27
360	411	4.695928	ACTACCGAATGCCTTCTCTTTTTC	59.304	41.667	0.13	0.00	0.00	2.29
362	413	4.287766	ACTACCGAATGCCTTCTCTTTT	57.712	40.909	0.13	0.00	0.00	2.27
425	479	1.009829	CCGGCTGCATTCTTCTGTAC	58.990	55.000	0.50	0.00	0.00	2.90
426	480	0.613260	ACCGGCTGCATTCTTCTGTA	59.387	50.000	0.00	0.00	0.00	2.74
518	620	1.063266	AGGGTTTCCTTGGCTGTTTCA	60.063	47.619	0.00	0.00	41.56	2.69
578	681	1.657181	CAAGTTTGGTGCGGCGTTC	60.657	57.895	9.37	1.43	0.00	3.95
579	682	1.658686	TTCAAGTTTGGTGCGGCGTT	61.659	50.000	9.37	0.00	0.00	4.84
580	683	1.658686	TTTCAAGTTTGGTGCGGCGT	61.659	50.000	9.37	0.00	0.00	5.68
581	684	0.526524	TTTTCAAGTTTGGTGCGGCG	60.527	50.000	0.51	0.51	0.00	6.46
582	685	1.864565	ATTTTCAAGTTTGGTGCGGC	58.135	45.000	0.00	0.00	0.00	6.53
583	686	4.586334	CAAAATTTTCAAGTTTGGTGCGG	58.414	39.130	0.00	0.00	41.34	5.69
974	1077	2.797278	GGCGGATCGGACAGATGGT	61.797	63.158	4.16	0.00	40.26	3.55
975	1078	2.029666	GGCGGATCGGACAGATGG	59.970	66.667	4.16	0.00	40.26	3.51
976	1079	2.355126	CGGCGGATCGGACAGATG	60.355	66.667	6.95	0.00	40.26	2.90
977	1080	4.286320	GCGGCGGATCGGACAGAT	62.286	66.667	9.78	0.00	43.51	2.90
1858	1961	3.250762	ACGACATGATTTATTGCATCCGG	59.749	43.478	0.00	0.00	0.00	5.14
1873	1976	6.802834	TCATTTTCATCACAATTCACGACATG	59.197	34.615	0.00	0.00	0.00	3.21
1874	1977	6.912082	TCATTTTCATCACAATTCACGACAT	58.088	32.000	0.00	0.00	0.00	3.06
2119	2222	4.264083	ACCATGGATCTCAAACTTGGTGAT	60.264	41.667	21.47	0.00	40.04	3.06
2145	2248	3.102515	GCACAGAGCAGCAAACATG	57.897	52.632	0.00	0.00	44.79	3.21
2282	2385	3.565307	TGCAGAACCTTGAATCCAACTT	58.435	40.909	0.00	0.00	0.00	2.66
2332	2435	4.742201	TTGAGAGGCGAGCGCACC	62.742	66.667	17.16	8.29	44.11	5.01
2579	2682	8.694540	CAACAATCAAAATCAGGGAATATGGTA	58.305	33.333	0.00	0.00	0.00	3.25
2583	2686	8.365060	TGACAACAATCAAAATCAGGGAATAT	57.635	30.769	0.00	0.00	0.00	1.28
2842	2945	7.776500	ATCAACCAGATGAACATGAATACATGA	59.224	33.333	15.53	0.00	44.49	3.07
2843	2946	7.937649	ATCAACCAGATGAACATGAATACATG	58.062	34.615	0.00	8.38	45.70	3.21
2844	2947	9.281371	CTATCAACCAGATGAACATGAATACAT	57.719	33.333	0.00	0.00	37.57	2.29
2845	2948	8.267183	ACTATCAACCAGATGAACATGAATACA	58.733	33.333	0.00	0.00	37.57	2.29
2846	2949	8.554528	CACTATCAACCAGATGAACATGAATAC	58.445	37.037	0.00	0.00	37.57	1.89
2847	2950	8.267183	ACACTATCAACCAGATGAACATGAATA	58.733	33.333	0.00	0.00	37.57	1.75
2848	2951	7.066645	CACACTATCAACCAGATGAACATGAAT	59.933	37.037	0.00	0.00	37.57	2.57
2849	2952	6.372381	CACACTATCAACCAGATGAACATGAA	59.628	38.462	0.00	0.00	37.57	2.57
2883	2986	9.618890	CAAATCAAAATAGTCTTATCAGGAGGA	57.381	33.333	0.00	0.00	0.00	3.71
2913	3017	3.895232	TGAGGAGCTTCCAAGTACATC	57.105	47.619	0.00	0.00	39.61	3.06
2992	3096	8.502161	AAAAAGAATCAAGTTAATACACGCAC	57.498	30.769	0.00	0.00	0.00	5.34
3120	3226	9.582431	CACGGAGAAACTATTCTAACAGAAATA	57.418	33.333	0.00	0.00	45.91	1.40
3153	3259	6.663953	TCCCTAGTGGTAAGCATATACTCATC	59.336	42.308	0.00	0.00	34.77	2.92
3180	3286	5.963594	ACTCTTTTGGTATTCCGTAGAGAC	58.036	41.667	16.07	0.00	37.93	3.36
3462	3817	3.504343	GCCTGGGTAGAATATACTCCCCT	60.504	52.174	0.00	0.00	37.03	4.79

Based at the University of Bristol with support from BBSRC.

AutoCloner maintained by Alex Coulton.